. Serum, C. Sputum, T. Fluid, and L. A. , Tissue Signature of the Patient's Agreement Remark: ??INH: Isoniazid, RFP: RifaRFPicin; SM: Streptomycin; EMB: Ethambutol

. Pyrazinamide, PAS: p-aminosalicylic acid; CSF: cerebrospinal fluid; LFA: Lavement Fluid from Alveolus; S: Sensitivity, R: Resistance Examples of spoligotyping results Genotype identification of Beijing province M. tuberculosis isolates with Spoligotyping

D. Alla-nd, G. E. Ka-lkut, A. R. Mo-ss, R. A. Mc-ad-a-m, J. A. Ha-hn et al., Transmission of Tuberculosis in New York City -- An Analysis by DNA Fingerprinting and Conventional Epidemiologic Methods, New England Journal of Medicine, vol.330, issue.24, pp.1710-1716, 1994.
DOI : 10.1056/NEJM199406163302403

D. D. Anh, M. W. Bo-rgdor-ff, L. N. Va-n, N. T. La-n, T. Va-n-gor-ko-m et al., Mycobacteriu m tubercu lo sis Beijing genotype emerging in Vietna m. E me rg I nfec t Dis, pp.302-307, 2000.

C. Ar-nold, N. Hor-ne, A. Under-wood, K. Ba-ster, and S. Gharbia, Evo lutio n o f shor t seq ue nce r epea ts in Mycobacteriu m tuberculo sis, FE MS Microbio l Lett, vol.2, pp.56-340, 2006.

M. A. Aziz, A. Wright, A. Laszlo, A. De-muynck, F. et al., Epid e mio lo gy o f a ntituber c ulo sis d r ug re sista nc e (the Globa l Project o n Anti -tub erc ulosis Dr ug Re sista nc e Surve illa nce): a n upda ted analysis. WHO/I nte r natio na l Unio n Aga inst Tube rc ulo sis And Lung Disease

L. Baker, T. N. Bro-wn, M. C. Drob-nie-wsk-i, and F. , Sile nt nucleotid e polymo rp hisms and a p hylo geny for Mycobacte rium tube rcu lo sis. E merg I nfect Dis, pp.1568-77, 2004.

A. Banerjee and M. Sugantino, T he mab A gene fro m the inhA opeer on o f Mycobacteriu m tuberculo sis e ncode s a 3 -ka toa c yl r ed ucta se that fa ils to co nfer iso niaz id resista nce, Microb iolo gy, pp.2697-2707, 1998.

J. Bauer, A. B. Ander-se-n, K. Kre-mer, and H. Ior-ner, Usefulness o f spo ligo typing To discriminate I S6110 lo w-cop y-nu mber Mycobacterium tubercu losis co mp le x str ains cultur ed in De n mar k, J Clin Microb iol, vol.37, pp.2602-2608, 1999.

P. Bifa-ni, B. Ma-the-ma, M. Ca-mpo, S. Mo-gha-ze-h, B. Nivin et al., Related to Multidrug-Resistant W Strain, Emerging Infectious Diseases, vol.7, issue.5, pp.842-850, 2001.
DOI : 10.3201/eid0705.010512

P. J. Bifa-ni, B. Ma-the-ma, N. E. Kurep-ina, and B. N. Kr-eiswir-th, Glo bal disseminatio n o f the Mycoba cterium tubercu losis W-Beijing fa mily strains, pp.45-52, 2002.

P. J. Bifa-ni, B. Ma-the-ma, Z. Liu, S. L. Mo-ghaz-e-h, B. Shop-sin et al., Identification of a W Variant Outbreak of <EMPH TYPE="ITAL">Mycobacterium tuberculosis</EMPH> via Population-Based Molecular Epidemiology, JAMA, vol.282, issue.24, pp.2321-2328, 1999.
DOI : 10.1001/jama.282.24.2321

R. Brosc-h, S. Gordo-n, T. Gar-nier, K. Eiglme-ier, W. Frigui et al., Genome plasticity of BCG and impact on vaccine efficacy, Proceedings of the National Academy of Sciences, vol.104, issue.13, pp.5596-5601, 2007.
DOI : 10.1073/pnas.0700869104

R. Brosc-h, S. V. Gordo-n, M. Mar-mie-sse, P. Brod-in, C. Uc-hrie-ser et al., A new evolutio nar y scenar io for the Mycobacterium tuberculo sis co mplex, P roc Natl Acad Sci, pp.3684-3693, 2002.

R. Brosc-h, A. S. Ym, S. V. Gordo-n, and S. T. Cole, T he evo lutio n o f mycobacter ial patho ge nicity: clue s fro m co mpar ative ge no mic s, pp.2-8, 2001.

K. Brude-y, J. R. Drisco-ll, L. Rigo-uts, W. M. Prodinger, A. Gori et al., Go me s, H She mya kin, I, Mycoba cterium tub erculo sis co mp le x ge ne tic dive rsity: mining the fo ur th inte rna tio nal spo ligo typing databa se (SpolDB4) for classificatio n, pop ulatio n genetics and epid emio lo gy. BM C Microb iol 6, 2006.

G. Ca-netti, W. Fo-x, and A. Kho-me-nko, Ad va nce s in tec hniq ue s o f te sting mycob acter ial dr ug sensitivity, and the use o f sensitivity tests in tuberculosis co ntrol progr ammes, pp.21-43

G. Ca-netti, S. Fro-ma-n, and J. Gros-set, M ycob acteria: laborator y method s for testing drug sensitivity and r esistance, Bull Wo rld Health Organ, vol.29, pp.565-578, 1963.

M. D. Ca-ve, K. D. Eise-nac-h, G. Te-mp-leto-n, M. Salfinger, G. Ure-k et al., Stab ility o f DNA fingerpr int patter n prod uced with I S6110 in strains o f Mycoba cterium tubercu losis, J Clin, vol.2, pp.262-268, 1994.

C. Cavuso-glu, S. Hilmio-glu, S. Guner-i, and A. Ilgic, Characterization of rpoB Mutations in Rifampin-Resistant Clinical Isolates of Mycobacterium tuberculosis from Turkey by DNA Sequencing and Line Probe Assay, Journal of Clinical Microbiology, vol.40, issue.12, pp.4435-4438, 2002.
DOI : 10.1128/JCM.40.12.4435-4438.2002

M. Y. Cha-n, M. Bo-rgdor-ff, and C. W. Yip, Se ve nty p erce nt o f the Mycoba cterium tubercuo sis iso la te s in Ho ng ko ng repr ese nt the Beiji ng geno type, pp.169-171, 2001.

M. Chand-ler and J. Mahillo-n, I nsertio n seq uences r evisited. American Society fo r Microb iolo gy, 2002.

P. J. Chin, C. C. Chiu, and R. Jo-u, Identification of Beijing Lineage Mycobacterium tuberculosis with Combined Mycobacterial Interspersed Repetitive Unit Loci 26, 31, and ETR-A, Journal of Clinical Microbiology, vol.45, issue.3, pp.1022-1025, 2007.
DOI : 10.1128/JCM.02036-06

L. S. Co-wa-n, L. Mo-sher, L. Die-m, J. P. Ma-sse-y, and J. T. Cra-wford, Variable -nu mber ta nd e m repeat typing o f My coba cte riu m tube rcu lo sis iso lates with lo w cop y numbers o f I S6110 b y using mycobacter ial intersper sed repetitive units, J Cli n Microbio l, vol.40, issue.1, pp.592-602, 2002.

F. Cr-uc-ia-ni, P. Sa-ntola-ma-z-za, P. She-n, V. Mac-a-ula-y, P. et al., Olc ker s, A. , Mod ia no A ba c k migr atio n fro m Asia to sub -Saharan Afr ica is supported b y high reso lutio n a na lysis of hu ma n Y-chro mo so me haplo typ es, Am J Hum Genet, vol.70, issue.002, pp.1197-1214

D. Be-e-nho-uwer, H. Lhiang, Z. Nne-s, and G. , Rapid detection of rifampicin resistance in sputum and biopsy specimens from tuberculosis patients by PCR and line probe assay, Tubercle and Lung Disease, vol.76, issue.5, pp.425-455, 1995.
DOI : 10.1016/0962-8479(95)90009-8

J. R. Drisco-ll, M. A. Cga-rr-y, and H. W. Taber, DNA typ ing o f a no nviable c ultur e o f Mycoba cterium tubercu losis in a ho meless she lter o utbre a k, J Clin Micr obiol, vol.37, issue.9, pp.274-279

M. Espa-sa, J. Go-nzalez-m-artin, and F. Alca-ide, Dir ec t de tec tion in clinic al sa mple s ofmultiple gene mutatio ns causing resistance o f Mycoba cterium tubercu losis to iso niaz id and rifa mpic in using fluorogenic pr obes, J Antimicrob Che mother, vol.55, issue.8, pp.60-65, 2005.

M. Fabre, J. Ko-ec-k, L. Fle-c-he, P. Simo-n, F. Her-ve et al., High Genetic Diversity Revealed by Variable-Number Tandem Repeat Genotyping and Analysis of hsp65 Gene Polymorphism in a Large Collection of "Mycobacterium canettii" Strains Indicates that the M. tuberculosis Complex Is a Recently Emerged Clone of "M. canettii", Journal of Clinical Microbiology, vol.42, issue.7, pp.3248-55, 2004.
DOI : 10.1128/JCM.42.7.3248-3255.2004
URL : https://hal.archives-ouvertes.fr/hal-01158318

E. J. Feil, B. C. Li, D. M. Aa-nense-n, W. P. Ha-na-ge, and B. G. Spra-tt, eBURST: inferr ing patter ns o f e vo lutio nar y desce nt a mo ng clusters of r ela ted b ac ter ial ge no typ e s fro m multilocus seq uence typ ing data, pp.1518-1530, 2004.

I. Filliol, J. R. Drisco-ll, D. Va-n-soolinge-n, B. N. Kre-is-wir-th, K. Kre-mer et al., Ra solo fo -Raza na mpara ny Te xie r-M a ugein, Snap shot o f mo ving a nd exp a nding c lo ne s o f Mycobacteriu m tubercu lo sis and their glob al distrib utio n assessed b y spoligotyp ing in an internatio nal stud y, pp.1963-70, 2003.

D. Alland, Glob al P hylo gen y o f Mycoba cte riu m tube rculo sis Ba sed o n Single Nucleotide Polymo rp hism ( SNP) Analys is: I nsights into Tub erculosis E volutio n, Phylo genetic Accuracy o f Other DNA Fingerprinting Syste ms, and Reco mmend atio ns for a Mini mal Standard SNP Set, J Bacter iol, vol.188, issue.75, pp.9-772, 2006.

I. Filliol, C. Sola, and N. Rastogi, Detection o f a previo usly unamplif ied spacer within the DR locus o f Mycobacterium tuberculo sis: e pide miolo gica l i mplica tio ns, J Clin Mic robiol, vol.38, pp.1231-1235, 2000.

R. D. Fle-isc-hma-nn, D. Alla-nd, J. A. Eise-n, L. Carp-enter, O. Hite et al., Fr a ser, C. M, 2002.

L. Flor-es, T. Va-n, S. Nara-ya-na-n, K. Der-ie-mer, M. Ka-to-ma-eda et al., Large Seq uence Polymo rp hisms Classify M ycobacter ium tuber culo sis Strains with Ancestral Spoligotyp ing Patter ns, J Clin M icrob iol, vol.45, issue.339, pp.3-5, 2007.

N. Fo-muko-ng, M. Be-ggs, H. Hajj, G. Te-mple-ton, K. Eise-nac-h et al., Differences in the prevalence of IS6110 insertion sites in Mycobacterium tuberculosis strains: low and high copy number of IS6110, Tubercle and Lung Disease, vol.78, issue.2, pp.109-110, 1997.
DOI : 10.1016/S0962-8479(98)80003-8

R. Fre-ssatti-cardo-so, R. C. Cooksey, and G. P. Mor-lock, Screening and Char acteriza tio n o f M utatio ns in I so niazid -Re sista nt My cobac te riu m tub ercu lo sis I solates Obtained in Brazil, Antimicrob ial Agents And C he mo ther ap y, pp.3373-3387, 2004.

R. Frothingham and W. A. Eeker-o-'co-nnell, Genetic d iver sity in the Mycobacteriu m tuberculo sis co mplex based o n variable number s of tand em DNA rep eats, pp.1189-1196, 1998.

D. Garc-ia-d-e-vied-ma, Rapid d ete ctio n o f r esista nce in Mycoba cte riu m tube rculo sis : a revie w discussing molecular appro aches. Clin M icrobio l I nfect 9, pp.349-59, 2003.

T. Gar-nier, K. Iglme-ier, J. Ca-mus, N. Nsoor, H. Pr-yor et al., T he co mplete ge no me seq uence o f Mycoba cterium bovis, 2003.

J. R. Glynn, J. Hitele-y, P. J. Bifa-ni, K. Kr-e-mer, and D. Va-n-soolinge-n, Wor ld wide occurrence o f Beijing/W strains o f Mycobacteriu m tub erculo sis : a syste matic re vie w, E merg I nfect Dis, vol.20, issue.8, pp.2-843

Y. O. Go-guet-de-la-sal-mo-nie-re, C. C. Kim, A. G. Tsola-ki, A. S. Ym, M. S. Sie-gr-ist et al., High-thro ughp ut method for detecting geno mic -deletio n po lymor phisms, J Clin Microb iol, vol.2, pp.2913-2921, 2004.

M. Go-yal, D. Yo-ung, Y. Zha-ng, P. A. Je-nkins, and R. J. Sha-w, P CR a mp lifica tio n o f va ria b le seq ue nce up strea m o f ka tG ge ne to subd ivid e str ains o f Mycoba cterium tubercu lo sis co mp lex, J Clin M icrobiol, vol.32, pp.3070-3071, 1994.

P. M. Groe-ne-n, A. E. Ho-te-n, D. Va-n-soo-lingen, and J. D. Van-e-mbden, Nature of DNA polymorphism in the direct repeat cluster of Mycobacterium tuberculosis; application for strain differentiation by a novel typing method, Molecular Microbiology, vol.85, issue.5, pp.1057-65, 1993.
DOI : 10.1016/0923-2508(92)90104-V

D. Gr-yad-uno-v, V. Ikha-ilovic-h, S. Lapa, N. Ro-udinskii, M. Do-nnikov et al., E valuatio n o f hybr idisatio n o n oligo nucleo tide microarr ays f or analysis o f drug-r esista nt Myc obacterium tubercu losis, Clin Microbiol I nfect, vol.11, issue.53, pp.1-9, 2005.

K. M. Guinn, M. J. Hic-ke-y, S. K. Ma-thur, K. L. Za-ke-l, J. E. Grotz-ke et al., Ind ivid ua l RD1 -regio n genes are req uir ed for export o f E S AT-6/CFP -10 and for vir ule nce o f Mycobacterium tuberculo sis, pp.359-370, 2004.

M. M. Guta-c-ker, B. Ma-the-ma, H. Soini, E. Sha-shkina, B. N. Kreis-wir-th et al., Strains from 4 Geographic Sites, The Journal of Infectious Diseases, vol.193, issue.1, pp.121-128, 2006.
DOI : 10.1086/498574

M. M. Guta-c-ker, B. Ma-the-ma, H. Soini, E. Sha-shkina, B. N. Kreis-wir-th et al., Strains from 4 Geographic Sites, The Journal of Infectious Diseases, vol.193, issue.1, pp.121-129, 2006.
DOI : 10.1086/498574

M. M. Guta-c-ker, J. C. Smoo-t, C. A. Migliacc-io, S. M. Ric-kle-fs, S. Hua et al., Ge no me -wid e analysis o f syno nymo us single nucleotid e polymo rp hisms in Mycobacteriu m tubercu losis co mp le x orga nisms: re solutio n o f ge netic r elatio nship s a mo ng clo se ly re la ted mi crobia l str ains, Genetics, vol.162, pp.1533-154, 2002.

M. C. Gutierre-z, S. Brisse, R. Brosc-h, M. Fabr-e, B. O-mais et al., Ancient origin and gene mosaicism o f the pro genitor o f Myco bacte riu m tuberculo sis, p.5, 2005.

M. H. Hazbo-n, Recent ad vances in mo lecular method s for ear ly diagno sis o f tuber culo si s and dr ug -resistant tuber culo sis, pp.149-62, 2004.

M. Heep, B. Br-a-nd-sta-tter, U. Rie-ger, N. Le-hn, E. Ric-hter et al., Fr eq uency o f rp oB mutatio ns inside and outside the cluster I r egion in rifamp in-resistant clinical Mycoba cterium tuberculo sis iso la te s, J Clin Microb iol, vol.9, pp.107-117, 2001.

H. F. Heer-sma, K. Kr-e-mer, and J. D. Va-n-e-mbd-e-n, Co mp uter analysis o f I S6110 RFLP patter ns of Mycobacteriu m tub erculo sis, pp.395-422, 1998.

L. Heifets, Co nventio nal method s for antimicrob ial susceptibility testing o f Mycoba cterium tubercu losis. Academic P ub lishers, 2000.

L. B. Heifets, Clinical mycobacter iolo gy. Dr ug suscep tib ility testing, Clin Lab Med, vol.16, pp.641-56, 1996.

P. W. Her-ma-ns, D. Va-n-soo-linge-n, J. W. Da-le, A. R. Schuite-ma, R. A. Ad-a-m et al., I nser tio n element I S986 fr o m Mycobacterium tuberculo sis : a useful tool for diagno sis and epidemio lo gy o f tuber culosis, J Clin Microbio, vol.8, pp.2051-2059, 1990.

P. W. Her-ma-ns, D. Va-n-soo-lingen, and J. D. Van-e-mbden, Chara cteriz atio n o f a major polymorp hic ta nde m r ep eat in Mycoba cterium tu bercu lo sis a nd its po te ntial use in the epidemiolo gy o f Mycoba cte riu m kan sa sii a nd Mycobacterium go rdonae, pp.4157-65, 1992.

D. Hille-ma-nn, M. We-ize-ne-gger, T. Kubica, E. Richter, and S. Nie-ma-nn, Use of the Genotype MTBDR Assay for Rapid Detection of Rifampin and Isoniazid Resistance in Mycobacterium tuberculosis Complex Isolates, Journal of Clinical Microbiology, vol.43, issue.8, pp.3699-703, 2005.
DOI : 10.1128/JCM.43.8.3699-3703.2005

A. Hir-sh, E. Tso-la-ki, A. G. De-rie-mer, K. Feld-ma-n, M. W. Sma-ll et al., Stable associatio n between strains o f Mycobacterium tu bercu lo sis and their human host populatio ns, Proc. Natl. Acad. Sci. USA 101, pp.71-4876, 2004.

P. R. Hunter and M. A. Ga-sto-n, Numerical index o f t he discr iminato r y ability o f typ ing syste ms: an applicatio n of Si mpso n's index o f diver sity, J Clin Microb iol, vol.26, pp.2465-2471, 1988.

P. Idigora-s, X. Ber-ista-in, A. Eta, D. Vice-nte, and E. Perez-trallero, Comparison of the Automated Nonradiometric Bactec MGIT 960 System with L??wenstein-Jensen, Coletsos, and Middlebrook 7H11 Solid Media for Recovery of Mycobacteria, European Journal of Clinical Microbiology & Infectious Diseases, vol.19, issue.5, pp.350-354, 2000.
DOI : 10.1007/s100960050492

R. Janse-n, J. D. Mbd-e-n, W. Ga-astra, and L. M. Sc-ho-uls, Identification o f genes that ar e assoc iated with DNA repeats in pro kar yo tes, pp.1565-1572, 2002.

W. W. Jiao, I. Mo-kro-uso-v, G. Z. Sun, M. Li, J. W. Liu et al., Molecular char acteristics o f r ifamp in and iso niazid resistant Mycoba cterium tuberculo sis str ains fro m Beijing, pp.814-823, 2007.

I. Joha-nse-n, V. Ho-mse-n, M. Marja-ma-ki, A. So-snovskaja, and B. Lund-gre-n, Rap id, auto ma ted, no nradio metric suscep tib ility te sting of Mycobacteriu m tub erculo sis co mp le x to fo ur first-line a ntitub erc ulo us dr ugs used in stand ard shor t -co ur se c he mo therap y. Dia gn Microb iol I nfect Dis, pp.103-110, 2004.

K. Ka-m, C. W. Yip, L. W. Tse, K. L. Wo-ng, T. K. La-m et al., Utility of Mycobacterial Interspersed Repetitive Unit Typing for Differentiating Multidrug-Resistant Mycobacterium tuberculosis Isolates of the Beijing Family, Journal of Clinical Microbiology, vol.43, issue.1, pp.306-309, 2005.
DOI : 10.1128/JCM.43.1.306-313.2005

A. Kaufhold, A. Podbielski, G. Bau-mgar-ten, M. Top, J. Schouls et al., Rap id Typ ing o f gro up A str eptococci b y the use o f DNA a mplific atio n a nd no n -ra dioa ctive allele -sp ecific oligo nucleotid e probes, FE MS Microbiol Lett, pp.19-26, 1994.

H. Kazue, A. Chiyojia, and T. Mitsuyoshi, Mutatio ns in the rpoB gene o f rifampin-re sista nt Mycoba cterium tubercu losis strains isolated mostly in Asian co untr ies and their rap id detectio n b y line prob e assay, J Clin Microb iol, vol.378, pp.2663-2666, 1999.

P. T. Ke-nt and G. P. Kub-ica, Pub lic Health M ycob acterio lo gy. A guid e for the Le vel I II Laborato r, 1985.

P. M. Khue, C. Tr-uffo-t-per-not, J. Te-xie-r-m-augein, V. Jarlier, and J. Robert, Ten year s o f prospective sur veillance of Mycobacteriu m tub erculo sis dr ug r esista nce in Fra nce, 1995.

S. Y. Kim, Y. J. Par-k, E. So-ng, H. Ja-ng, C. Kim et al., E valuatio n o f the Co mb iChip M ycobacter ia Dr ug-Re sista nce de te c tio n DNA c hip for ide ntifying mutatio ns associated with resistance to iso niazid and r ifamp, pp.6-203

R. Koch, Die Aetio lo gie der Tub erculo se, Klinische Wochenschr, vol.19, pp.221-230, 1882.

S. Y. Ko-valev, E. Y. Ka-mae-v, M. A. Kr-a-vc-he-nko, N. E. Kurep-ina, and S. N. Skor-nia-ko-v, Genetic analysis o f Mycobacteriu m tuberculo sis strains isola ted in Ural regio n, Russia n Feder atio n, b y MI RU -VNT R geno typing. I nt, J Tuber c Lung Dis, vol.9, pp.746-751, 2005.

K. Kre-mer, C. Ar-nold, A. Ca-ta-ldi, M. C. Gutierrez, W. H. Haa-s et al., Discriminatory Power and Reproducibility of Novel DNA Typing Methods for Mycobacterium tuberculosis Complex Strains, Journal of Clinical Microbiology, vol.43, issue.11, pp.5628-5666, 2005.
DOI : 10.1128/JCM.43.11.5628-5638.2005

K. Kremer, D. Van-soolingen, R. Fro-thingha-m, W. H. Haa-s, P. W. Her-ma-ns et al., Co mpariso n o f method s b ased o n differ ent mo lecular epidemiolo gical mar ker s for typ ing o f Mycoba cterium tubercu losis co mp le x str ains: inter labor ator y stud y o f discriminator y po wer and reprod ucibility, J Clin Microbiol, vol.37, pp.2607-2625, 1999.

A. Kr-uuner, S. E. Ho-ffner, H. Silla-stu, M. Da-nilo-vits, K. Le-vina et al., Spr ead o f dr ug-re sista nt p ulmo nar y tub erculosis in E sto nia, J Clin M icrob iol, vol.39, issue.333, pp.9-45

N. Kurepina, E. Likho-shvay, E. Shashkina, B. Mathema, K. Kre-mer et al., Targeted hybrid ization o f I S6110 fingerprints identifies the W-B eijing Mycobacteriu m tub erculo sis strains a mo ng clinic al isolate s, J Clin Mic, vol.20, issue.43, pp.5-2148

N. E. Kurepina, S. Sr-ee-va-tsa-n, B. B. Plika-ytis, P. J. Bifa-ni, N. D. Co-nnell et al., Characterization of the phylogenetic distribution and chromosomal insertion sites of five IS6110elements inMycobacterium tuberculosis: non-random integration in thednaA???dnaNregion, Tubercle and Lung Disease, vol.79, issue.1, pp.31-42, 1998.
DOI : 10.1054/tuld.1998.0003

K. F. Laser-so-n, L. Osor-io, and J. D. Sheppard, Clinical and pr ogra mmatic mis management rather than co mmunity o utbreak as the cause o f chro nic, drug-r e sista nt tub erculosis in B uenaventura, Co lo mbia, 1998. I nt J Tub erc, Lung Dis, vol.67, pp.3-683, 2000.

L. Flèc-he, P. Fabre, M. Denoeud, F. Koeck, J. L. Vergnaud et al., High reso lutio n, o n-line ide ntifica tio n o f stra ins fro m the Mycobacteriu m tuberculo sis co mp le x b ased o n ta nde m repea t typ ing, BMC Microbiology, vol.2, issue.1, p.37, 2002.
DOI : 10.1186/1471-2180-2-37

L. Flè-c-he, P. Ha-uc-k, Y. Onte-nie-nte, L. Pr-ie-ur, A. De-noe-ud et al., A tandem repeats database for bacter ial ge no me s: applica tio n to the ge no typing o f Ye rsin ia pe stis a nd Ba cillu s an thra cis, 2001.

A. S. Lee, A. S. Teo, and S. Y. Wo-ng, No vel mutatio ns in nd h in iso niazid -resistant Mycoba cterium tubercu losis iso lates, Antimicro b Agents Chemo ther 45, pp.2157-2166, 2001.

E. Legrand, I. Filliol, C. Sola, and N. Rasto-gi, Use o f spo ligo typing to stud y the evolutio n of the d irec t r epeat lo cus b y I S6110 transpositio n in Mycoba cte rium tub ercu lo sis, J Clin Microb iol, vol.9, issue.001, pp.1595-1604

W. M. Li, S. M. Wa-ng, C. Y. Liu, Y. H. She-n, G. M. Zha-ng et al., Molecular ep idemiolo gy o f Mycoba cterium tubercu losis in China: a na tio n wide ra ndo m sur ve y in 20 00, Int J Tuber c Lung Dis, vol.9, pp.1314-1323, 2005.

X. Li, Y. Zha-ng, X. She-n, G. She-n, X. Gui et al., Transmissio n o f drug-r esistant tuberculo sis amo ng tr eated patients in Shangha i, China. J I nfect Dis, vol.195, pp.864-869, 2007.

J. H. Liu, L. S. Zha-ng, Z. G. Liu, M. X. Hua-ng, X. Q. Zhao et al., Stud y on the c hara cter istic s o f muta tio n o n Mycobac te riu m tub erculo sis rifa mpicin-r e sista nce gene, Zho nghua Liu Xing B ing Xue Za Zhi, pp.73-976, 2006.

B. Lop-ez, D. Aguilar, H. Orozco, M. Urger, C. Esp-itia et al., A mar ked d ifference in patho ge ne sis a nd immun e re spo nse, pp.30-37, 2003.

X. Ma, H. Wa-ng, Y. De-ng, Z. Liu, Y. Xu et al., rpoB Gene mutatio ns and molecular char acterizatio n of r ifamp in -re sista nt Mycobacterium tuberculo sis isolates fr o m Shando ng Province, China, J Clin Microbiol, vol.4, issue.4, pp.3409-3412, 2006.

J. Magdalena, A. Vachee, P. Supply, and C. Locht, Identificatio n o f a ne w DNA regio n spec ific for me mber s o f Mycoba cterium tubercu losis co mplex, J Clin M icrobiol, vol.36, pp.937-980, 1998.

G. G. Ma-ha-ira-s, P. J. Sabo, M. J. Hic-ke-y, D. C. Singh, and C. K. Sto-ver, Molecular analysis of genetic differences between Mycobacterium bovis BCG and virulent M. bovis., Journal of Bacteriology, vol.178, issue.5, pp.1274-1282
DOI : 10.1128/jb.178.5.1274-1282.1996

M. Mar-mie-sse, P. Brod-in, C. Buc-hrie-ser, C. Gutie-r-rez, N. Simo-e-s et al., Macro -arra y a nd bio info r matic a nalyse s r e vea l mycob ac ter ial 'core ' ge ne s, variatio n in the E SAT-6 ge ne fa mily a nd ne w p hylo ge netic ma r ker s for the Mycoba cterium tubercu losis co mplex, pp.483-96, 2004.

B. Mathe-ma, N. E. Kur-epina, P. J. Ifa-ni, and B. N. Kr-eiswir-th, Molecular Epidemiology of Tuberculosis: Current Insights, Clinical Microbiology Reviews, vol.19, issue.4, pp.658-85, 2006.
DOI : 10.1128/CMR.00061-05

C. E. Ma-us, B. B. Plika-ytis, and T. M. Shinnic-k, M utatio n o f tlyA co nfer s capre o mycin resista nce in Mycobac te riu m tub erculo sis, Antimicrob Agents Chemo ther 49, pp.571-578

E. Mazar-s, S. Le-sjea-n, A. L. Banuls, M. Gilber-t, V. Vinc-e-nt et al., High-r eso lutio n minisatellite -ba sed typ ing as a po rtable approach to glo bal a na lysis o f Myco bacte riu m tube rculo sis mo lec ular epid e mio lo gy, Proc Na tl Acad Sci U S A 98, pp.1901-1907, 2001.

T. D. Mchugh and S. H. Gillesp-ie, No nr ando m asso ciatio n o f I S6110 and Mycobacteriu m tuberculo sis: i mplica tio ns for mo le c ular epid e miolo gica l stud ie s, J Clin Microb iol 3, vol.6, pp.1410-1413, 1998.

L. Mie-se-l, T. R. We-isbord, and J. Amarc-inke-vicie-ne, NADH d ehydro ge na se d e fec ts confer iso niaz id re sista nce a nd co nditio na l letha lty in Mycoba cte rium S megma tis, pp.2459-2467, 1998.

I. Mokro-uso-v, W. W. Jiao, V. Valc-he-va, A. Vya-zo-va-ya, T. Otte-n et al., Rapid Detection of the Mycobacterium tuberculosis Beijing Genotype and Its Ancient and Modern Sublineages by IS6110-Based Inverse PCR, Journal of Clinical Microbiology, vol.44, issue.8, pp.2851-2857, 2006.
DOI : 10.1128/JCM.00705-06

I. Mokro-uso-v, H. M. Ly, T. Otte-n, N. N. La-n, B. Vyshne-vskyi et al., Or igin and pr imar y disper sal o f the Mycobacteriu m tuberculo sis Beijing ge no type : clue s fro m hu ma n p hylo geo gr ap hy, Ge no me Re s 15, pp.1357-64, 2005.

I. Mokro-uso-v, O. Nar-vska-ya, T. Otte-n, A. Vyazo-va-ya, E. Lime-sc-he-nko et al., Phylogenetic reconstruction within Mycobacterium tuberculosis Beijing genotype in northwestern Russia, Research in Microbiology, vol.153, issue.10, pp.629-666, 2002.
DOI : 10.1016/S0923-2508(02)01374-8

N. Morcillo, M. Zumar-ra-ga, A. Alito, A. Dol-ma-nn, L. Sc-ho-uls et al., A lo w cost, ho me -mad e, r ever se -line b lot hybrid isatio n a ssa y for rapid de tec tio n o f ri fampicin r esistance in Myco bacte riu m tub erculo sis, Int J Tuberc Lung Dis, vol.6, pp.959-65, 2002.

M. Morga-n, S. Ka-la-ntr-i, L. Flor-es, and M. Pai, A co mme rc ial line probe assa y for the r apid detec tio n o f rifa mpicin r esista nc e in Mycobacterium tuberculo sis : a systematic r eview and me ta -analysis, p.62, 2005.

S. Mosto-wy, D. Co-usins, J. Brinkma-n, A. Ara-naz, and M. A. Be-hr, Complex, The Journal of Infectious Diseases, vol.186, issue.1, pp.74-80, 2002.
DOI : 10.1086/341068

J. M. Musser, Ant imicrob ial a ge nt re sistance in mycob acteria: molec ular ge netic insights, Clin Microb iol Rev, vol.8, issue.4, pp.96-514, 1995.

W. Namwat, P. Luangsuk, and P. Palittapo-ngar-npim, T he genetic diversity o f Mycobacterium tuberculo sis stra ins in T ha ila nd stud ied b y a mplifica tio n o f DNA segments co ntaining direc t rep etitive seq ue nc es. I nt J Tuber c, Lung Dis, vol.2, pp.153-162, 1998.

V. V. Niko-la-ye-vskyy, T. J. Br-o-wn, Y. I. Baz-ho-ra, A. A. Asmo-lov, Y. M. Balaba-nova et al., Mo lecular epidemiolo gy and prevalence o f mutatio ns co nferri ng rifa mpicin and iso nia zid re sista nc e in Mycobacteriu m tuberculo sis stra ins fro m the so uther n Ukra ine. Clin Microb iol I nfect, pp.129-138, 2007.

J. C. Palo-mino, Nonconventional and new methods in the diagnosis of tuberculosis: feasibility and applicability in the field, European Respiratory Journal, vol.26, issue.2, pp.339-50, 2005.
DOI : 10.1183/09031936.05.00050305

J. C. Palo-mino, Newer diagnostics for tuberculosis and multi-drug resistant tuberculosis, Current Opinion in Pulmonary Medicine, vol.12, issue.3, pp.172-180, 2006.
DOI : 10.1097/01.mcp.0000219265.50310.9b

G. Pfyffe-r, D. Bo-na-to, and A. Ebra-himz-ade-h, M ultice nter lab orator y va lid atio n o f suscep tib ility te sting o f Mycoba cterium tubercu losis a gainst c la ssic al se cond -line and ne wer antimicrobial dr ugs b y using the radio metric B ACT E C 460 technique and the proportio n method with solid med ia, J Clin Micr obiol, vol.37, pp.3179-86, 1999.

G. E. Pfyffe-r, H. M. We-lsc-her, P. Kissling, C. Cie-slak, M. J. Ca-sa-l et al., Co mpar iso n of the M ycobacteria Gro wth I nd icator Tube (M GIT ) with radio metric and solid culture for reco ver y o f acid-fast b acilli, J Clin M icrobiol, vol.35, pp.364-372, 1997.

B. B. Plika-ytis and J. L. Marde-n, Cr a wfo rd, 1994.

L. Qia-n, J. D. Va-n-e-mbd-e-n, A. G. Va-n-der-za-nd-e-n, E. F. We-lte-vrede-n, H. Dua-nmu et al., Retro spective analysis o f the Beijing family o f Mycobacteriu m tubercu lo sis in preser ved lung tissues, J Clin Microbio l, vol.37, pp.471-475, 1999.

S. Ramas-wamy and J. M. Usser, Molecular genetic basis of antimicrobial agent resistance inMycobacterium tuberculosis: 1998 update, Tubercle and Lung Disease, vol.79, issue.1, pp.3-29, 1998.
DOI : 10.1054/tuld.1998.0002

M. C. Raviglio-ne, T he T B epid emic fro m Tub erculo sis, pp.4-14, 1992.

M. B. Re-ed, P. Do-me-ne-c-h, C. Ma-nca, H. Su, A. K. Kre-is-wirth et al., A glycolip id o f hyp er vir ulent tub erculosis str ains that inhib its the innate immune r espo nse, Nature, vol.3, issue.431, pp.84-91, 2004.

M. B. Re-ed, S. Ga-gne-ux, K. Der-ie-mer, P. M. Sma-ll, and C. E. Barr-y, The W-Beijing Lineage of Mycobacterium tuberculosis Overproduces Triglycerides and Has the DosR Dormancy Regulon Constitutively Upregulated, Journal of Bacteriology, vol.189, issue.7, pp.2583-258, 2007.
DOI : 10.1128/JB.01670-06

J. Re-ngaraja-n, C. M. Sa-sse-tti, V. Narod-itska-ya, A. Slo-utsky, B. R. Bloo-m et al., The folate pathway is a target for resistance to the drug para-aminosalicylic acid (PAS) in mycobacteria, Molecular Microbiology, vol.236, issue.1, pp.275-82, 2004.
DOI : 10.1111/j.1365-2958.2004.04120.x

H. L. Rieder, M. Cho-nde, H. Urb-a-ncz-ik, R. La-sz-lo, A. Kim et al., T he Pub lic Health Ser vice Natio nal Tuberculo sis R efere nc e Laborato r y a nd the Na tiona l Laborato r y Net wor k Minimu m Req uire me nts, Ro le a nd Opera tio n in a Lo w-I nco me Co untr y I nter natio nal Unio n Against Tuber culosis and Lung Disease, 1998.

G. D. Rober-ts, N. L. Good-ma-n, L. Heifets, H. W. La-rsh, T. H. Lind-ner et al., E valuatio n o f the B ACT EC rad io metri c method for reco ver y o f mycob acter ia and dr ug suscep tib ility testing o f Mycoba cterium tuberculo sis fro m a cid -fast smea r-po sitive sp ecimens, J Clin M, vol.18, pp.689-96, 1983.

S. Ror-ing, A. N. Sco-tt, G. He-winso-n, R. Ne-ill, S. D. Skuce et al., E valuatio n o f var iab le numb er tandem repeat (VNT R) loci in molecular typing o f Myco bacteriu m bovis iso la te s fro m Ir ela nd, Vet M icrob iol, vol.20, issue.101, pp.4-65

M. Ruiz, M. Torres, A. Llano-s, A. Arro-yo, J. Palo-ma-re-s et al., Direc t de tec tio n o f rifamp in-a nd iso nia zid -resista nt Mycoba cterium tuberculo sis in aur a mine -r hodaminepo sitive sp utum specimens b y r eal -ti me P CR, J Clin Microb iol, vol.2, pp.1585-1594, 2004.

S. Rusc-h-gerde-s, G. E. Pfyff-er, M. Ca-sa-l, M. Cha-d-wic-k, and S. Siddiq-i, Multicenter Laboratory Validation of the BACTEC MGIT 960 Technique for Testing Susceptibilities of Mycobacterium tuberculosis to Classical Second-Line Drugs and Newer Antimicrobials, Journal of Clinical Microbiology, vol.44, issue.3, pp.688-92, 2006.
DOI : 10.1128/JCM.44.3.688-692.2006

A. Sajd-uda, A. Brzo-stek, M. Popla-wska, E. Augus-tyno-wicz-kopec, Z. Zwolska et al., Molecular char acterizatio n o f rifa mpin-a nd iso niaz id -re sista nt Myco bacte riu m tube rculo sis strains isolated in Poland, J Clin Microb iol, vol.2, pp.2425-2456, 2004.

F. B. Seibert, T he isolatio n and proper ties o f the p urified protein derivative o f tuber culin, p.713, 1934.

I. C. Sha-mp-uta, L. Rigo-uts-and, and F. Por-taels, Molecular genetic method s for d iagno sis and antibio tic resistance detectio n o f mycobacteria fro m clinical sp ecimens, pp.728-52, 2004.

U. B. Singh, N. Sur-e-sh, N. V. Bha-nu, J. Arora, H. Pant et al., Predo minant tuberculo sis spoligotyp es, pp.1138-1180, 2004.

P. M. Sma-ll, P. C. Hope-we-ll, S. P. Singh, A. Pa-z, J. Parso-nnet et al., The Epidemiology of Tuberculosis in San Francisco -- A Population-Based Study Using Conventional and Molecular Methods, New England Journal of Medicine, vol.330, issue.24, pp.1703-1712, 1994.
DOI : 10.1056/NEJM199406163302402

I. Smith, Mycobacterium tuberculosis Pathogenesis and Molecular Determinants of Virulence, Clinical Microbiology Reviews, vol.16, issue.3, pp.463-96, 2003.
DOI : 10.1128/CMR.16.3.463-496.2003

N. H. Smith, J. Dale, J. Nwa-ld, S. Pal-mer, S. V. Gor-don et al., The population structure of Mycobacterium bovis in Great Britain: Clonal expansion, Proceedings of the National Academy of Sciences, vol.100, issue.25, pp.15271-15276, 2003.
DOI : 10.1073/pnas.2036554100

N. Smittipa-t, P. Billa-ma-s, M. Palittapo-ngar-npim, A. Ho-ng-on, M. M. Te-mu et al., Polymorp hism o f var iab le -numb er ta nde m repe ats a t multip le lo ci in My cobacteriu m tub erculo sis, J Clin M, vol.43, issue.2, pp.5-5034

N. Smittipat and P. Palittapo-ngar-np-im, Identification of possible loci of variable number of tandem repeats in Mycobacterium tuberculosis, Tubercle and Lung Disease, vol.80, issue.2, pp.69-76, 2000.
DOI : 10.1054/tuld.2000.0236

S. Sree-vatsa-n, X. Pa-n, K. E. Stoc-kba-uer, N. D. Co-nne-ll, B. N. Kr-eiswir-th et al., Restricted str uctur al gene po lymor phism in the Mycobacterium tuberculo sis co mp le x indica te s e vo lutio nar ily rec e nt globa l d isse mina tio n, Proc Natl Acad Sc i U S A 94, pp.9869-74, 1997.

K. Srivasta-va, R. Das, and P. Jakhmo-la, Cor relatio n o f muta tio ns de tec ted b y INNO -LIPA with levels of r ifamp in resistance in Mycobacteriu m tubercu losis. I ndia n, J Med Res, vol.8, pp.100-105, 2004.

P. Supply, C. Allix, S. Le-sjea-n, M. Cardo-so-oelemann, S. Rusch-gerde-s et al., Proposal for Standardization of Optimized Mycobacterial Interspersed Repetitive Unit-Variable-Number Tandem Repeat Typing of Mycobacterium tuberculosis, Journal of Clinical Microbiology, vol.44, issue.12, pp.4498-4510, 2006.
DOI : 10.1128/JCM.01392-06

P. Supply, S. Lesje-a-n, E. Sa-vine, K. Kre-mer, D. Va-n-soo-linge-n et al., Automated High-Throughput Genotyping for Study of Global Epidemiology of Mycobacterium tuberculosis Based on Mycobacterial Interspersed Repetitive Units, Journal of Clinical Microbiology, vol.39, issue.10, pp.3563-71, 2001.
DOI : 10.1128/JCM.39.10.3563-3571.2001

P. Supply, E. Maza-rs, S. Lesjea-n, V. Vince-nt, B. Gicq-uel et al., Variab le hu ma n minisa te llite -like regio ns in the Mycobacteriu m tuberculo sis ge no me, pp.762-71, 2000.

A. Tele-nti, N. Ho-nore, and C. Bernasco-ni, Geno typic assess ment o f iso niazid rifamp in resistance in Mycobacte riu m tub erculo sis : a b lind stud y a t re fer ence labora tor y level, J Clin M icrob iol, vol.35, pp.719-723, 1997.

T. Hierr-y, D. Ca-ve, M. D. Eise-na-c-h, K. D. Cra-wfo-rd, J. T. Bate-s et al., IS6110, an I S -like element o f Mycoba, 1990.

A. G. Tsola-ki, S. Ga-gne-ux, A. S. Ym, Y. O. Go-guet-d-e-la-sa-lmo-niere, and B. N. Kreiswirth, Genomic Deletions Classify the Beijing/W Strains as a Distinct Genetic Lineage of Mycobacterium tuberculosis, Journal of Clinical Microbiology, vol.43, issue.7, pp.3185-91, 2005.
DOI : 10.1128/JCM.43.7.3185-3191.2005

A. G. Tsola-ki, A. E. Hir-sh, K. De-rie-me-r, J. A. Nc-iso, M. Z. Wo-ng et al., Functional and evo lutio nar y ge no mic s o f Mycoba cterium tub erculosis: insights fro m geno mic deletio ns in 100 strains, pp.4865-70, 2004.

N. T. Tuberc-ulosis, Repor t o n fo ur th natio na l ep id e miolo gic al sa mpling sur ve y o f tube rc ulo sis, Chin J. Tuberc Resp ir Dis, vol.25, issue.1, pp.3-7, 2002.

R. Va-n-cre-ve-l, R. H. Ne-lwa-n, W. Le-nne, Y. Ve-erara-gu, A. G. Va-n-d-er-za-nden et al., Beijing Genotype Strains Associated with Febrile Response to Treatment, Emerging Infectious Diseases, vol.7, issue.5, pp.880-883, 2001.
DOI : 10.3201/eid0705.017518

A. G. Va-n-der-za-nde-n, A. H. Hoentje-n, F. G. Heilma-nn, E. F. Welte-vred-e-n, L. M. Sc-ho-uls et al., Simultaneous detection and strain differentiation of Mycobacterium tuberculosis complex in paraffin wax embedded tissues and in stained microscopic preparations, Molecular Pathology, vol.51, issue.4, pp.209-223, 1998.
DOI : 10.1136/mp.51.4.209

A. G. Va-n-der-za-nde-n, K. Kre-mer, L. M. Sc-ho-uls, K. Caimi, A. Ca-ta-ldi et al., Improvement of Differentiation and Interpretability of Spoligotyping for Mycobacterium tuberculosis Complex Isolates by Introduction of New Spacer Oligonucleotides, Journal of Clinical Microbiology, vol.40, issue.12, pp.4628-4667, 2002.
DOI : 10.1128/JCM.40.12.4628-4639.2002

J. D. Va-n-e-mbde-n, M. D. Ca-ve, J. T. Cr-a-wford, J. W. Dale, K. D. Nac-h et al., Stra in id e ntificatio n o f Mycoba cterium tubercu losis b y DNA fingerp rinting: r eco mmendatio ns for a stand ardized methodolo gy, J Clin Microbiol, vol.31, pp.406-415, 1993.

J. D. Va-n-e-mbde-n, T. Va-n-gor-ko-m, K. Kre-mer, R. Janse-n, B. A. Va-n-de-r-ze-ijst et al., Genetic Variation and Evolutionary Origin of the Direct Repeat Locus of Mycobacterium tuberculosis Complex Bacteria, 1. va n Kli nger e n, pp.2393-2433, 2000.
DOI : 10.1128/JB.182.9.2393-2401.2000

D. Va-n-soo-linge-n, L. Qia-n, P. E. De-ha-a-s, J. T. Do-ugla-s, H. Traore et al., Predo minance of a single ge no type o f Mycobacterium tuberculo sis in co untries o f east Asia, J Clin Microbiol, vol.33, pp.3234-3242, 1995.

J. Veen, Microepidemics of tuberculosis: the stone-in-the-pond principle, Tubercle and Lung Disease, vol.73, issue.2, pp.73-76, 1992.
DOI : 10.1016/0962-8479(92)90058-R

G. Vergnaud and C. Pour-cel, M ultiple Locus VNT R (Variable Numb er o f Tandem Re pe at) Analysis Syste ma tic s, a nd Po pulatio n Str uc ture o f Pro kar yote s, Mo lec ular Id e ntification, pp.83-104, 2006.

Z. H. Ya-ng, K. Ija-z, J. H. Ba-tes, K. D. Eise-nac-h, and M. D. Ca-ve, Spo ligotyp ing a nd polymorp hic GC-r ic h r e petitive seq ue nce finger printing o f Mycoba cterium tub erculo sis str ains ha ving few copies o f I S6110, J Clin Micr obiol, vol.38, pp.3572-3578, 2000.

Y. Zha-ng, T. Garbe, and D. Yo-ung, Transfor matio n with katG restore siso niaz id -sensitivity in Mycobacterium Tubercu lo sis isolates resisant to a r ange o f drugco ntratio ns, Mol Microbiol, pp.521-524, 1993.

Y. Zhang, C. Vilcheze, and W. R. Jacobs, Mechanisms o f dr ug resistance in Mycoba cte riu m tuberculo sis Amer ican Society for M icrob iolo gy, 2005.